During DNA replication - (Jun/03/2006 )

DNA replication needs the presence of a primer with a free 3' end to initiate nucleotide extension,
but i'm thinking why RNA primer is used here instead of a DNA primer, anyway the primer will be removed later???!!

waiting for ur replies...

There are no enzymes which create new DNA strands without extending a 3' end. Primase, however, can create a complementary region of RNA with no free 3' end. It is used to prime creation of Okazaki fragments, and as you suggest, the RNA is later replaced with DNA and the fragments ligated. Google "primase" and find more info.

thanx phage434..for your fast reply

but what about the RNA primer?

There is none. Primase creates an RNA region complementary to the opposite DNA strand with no primer.

hi

lets get one thing straight....during natural dna replication, an "rna primer" is synthesized on BOTH strands, not just the one with okazaki fragments. the reason is that dna polymerase is, unfortunately, only a chain extension enzyme, and NOT a chain initiation enzyme. thus dna pol can only extend what is already there, and what is already there is the short rna fragmet put in place by primase, since primase is a rna pol, and rna pols CAN nitiate new strands.

as the dna opens up and a replication fork is created, you have two single strands, one with a free 3' end and the other with a free 5' end. since dna replication proceeds in the 5'-3' direction, the primase puts in a single short primer on the template with the free 3' end, thus initiating the 5'-3' replication, that is taken over by the dna pol after the primase ends putting in the rna primer. hence this "leading strand" does have an rna primer, but only one, since along the length of the rest of the template, there is no problem of polarity.

on the other strand, the lagging strand, what is exposed is the template 5' end and hence the new strand cannot start in the 3'-5' direction. thus the primase starts to put in the rna primer at the Y end of the fork. hence a short fragment is synthesized in the 5'-3' direction that is made up of the primer, and the rest of the dna is synthesized by the dna pol. in the meantime, unwinding has gone up further to extend the fork, and so the primase starts a new fragment at the Y end of the fork. this gives another short fragment. these short ragments are the okazaki fragments and each okazaki fragment has an rna primer at its beginning.

thus the lagging strand has many rna primers, while the leading strand has just one........

- viv

DNA replication needs the presence of a primer with a free 3' end to initiate nucleotide extension,
but i'm thinking why RNA primer is used here instead of a DNA primer, anyway the primer will be removed later???!!

waiting for ur replies...

thanx everybody...

it becomes clear now

what i just know is that primase is a rna polymerase